Support for py38 and Cartopy 0.19 (#4130)

* mpl 3.4.1 updates (#4087) * replace most recent hashes (#4112) * Corrected plot_anomaly_log_colouring for new Matplotlib linscale rules. (#4115) * Cartopy 0.19 updates (#4128) * Use assertArrayAllClose for sqrt test (#4118) * using AllClose for sqrt test * Omitting the checksum from test cml * use ArrayAllClose (rebase reset it?) * Iris py38 (#3976) * support for py38 * update CI and noxfile * enforce alphabetical xml element attribute order * full tests for py38 + fix docs-tests * add whatsnew entry * update doc-strings + review actions * Alternate xml handling routine (#29) * all xml tests pass for nox tests-3.8 * restored docstrings * move sort_xml_attrs * make sort_xml_attrs a classmethod * update sort_xml_attr doc-string Co-authored-by: Bill Little <bill.james.little@gmail.com> * add jamesp to whatsnew + minor tweak Co-authored-by: James Penn <james@jamespenn.co.uk> * reinstate black and nox links * Linkcheck update (#4104) * Updated links * Added login remark * Removed extra space * change to kick cirrus * kick cirrus * test verbose on cirrus * Removed test settings. Co-authored-by: Bill Little <bill.james.little@gmail.com> Co-authored-by: Martin Yeo <40734014+trexfeathers@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: James Penn <james.penn@metoffice.gov.uk> Co-authored-by: James Penn <james@jamespenn.co.uk> Co-authored-by: tkknight <2108488+tkknight@users.noreply.github.com>
SciTools · May 13, 2021 · e537afa · e537afa
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diff --git a/.cirrus.yml b/.cirrus.yml
@@ -120,6 +120,8 @@ test_minimal_task:
       PY_VER: 3.6
     env:
       PY_VER: 3.7
+    env:
+      PY_VER: 3.8
   name: "${CIRRUS_OS}: py${PY_VER} tests (minimal)"
   container:
     image: gcc:latest
@@ -143,6 +145,8 @@ test_full_task:
       PY_VER: 3.6
     env:
       PY_VER: 3.7
+    env:
+      PY_VER: 3.8
   name: "${CIRRUS_OS}: py${PY_VER} tests (full)"
   container:
     image: gcc:latest
@@ -172,9 +176,7 @@ gallery_task:
   << : *CREDITS_TEMPLATE
   matrix:
     env:
-      PY_VER: 3.6
-    env:
-      PY_VER: 3.7
+      PY_VER: 3.8
   name: "${CIRRUS_OS}: py${PY_VER} doc tests (gallery)"
   container:
     image: gcc:latest
@@ -204,7 +206,7 @@ doctest_task:
   << : *CREDITS_TEMPLATE
   matrix:
     env:
-      PY_VER: 3.7
+      PY_VER: 3.8
   name: "${CIRRUS_OS}: py${PY_VER} doc tests"
   container:
     image: gcc:latest
@@ -240,7 +242,7 @@ linkcheck_task:
   << : *CREDITS_TEMPLATE
   matrix:
     env:
-      PY_VER: 3.7
+      PY_VER: 3.8
   name: "${CIRRUS_OS}: py${PY_VER} doc link check"
   container:
     image: gcc:latest

diff --git a/docs/iris/gallery_code/general/plot_anomaly_log_colouring.py b/docs/iris/gallery_code/general/plot_anomaly_log_colouring.py
@@ -68,14 +68,14 @@ def main():
     # Create a 'logarithmic' data normalization.
     anom_norm = mcols.SymLogNorm(
         linthresh=minimum_log_level,
-        linscale=0,
+        linscale=0.01,
         vmin=-maximum_scale_level,
         vmax=maximum_scale_level,
     )
     # Setting "linthresh=minimum_log_level" makes its non-logarithmic
     # data range equal to our 'zero band'.
-    # Setting "linscale=0" maps the whole zero band to the middle colour value
-    # (i.e. 0.5), which is the neutral point of a "diverging" style colormap.
+    # Setting "linscale=0.01" maps the whole zero band to the middle colour value
+    # (i.e., 0.5), which is the neutral point of a "diverging" style colormap.
 
     # Create an Axes, specifying the map projection.
     plt.axes(projection=ccrs.LambertConformal())

diff --git a/docs/iris/src/developers_guide/gitwash/git_links.inc b/docs/iris/src/developers_guide/gitwash/git_links.inc
@@ -28,6 +28,6 @@
 .. _git config: http://schacon.github.com/git/git-config.html
 
 .. _linux git workflow: http://www.mail-archive.com/dri-devel@lists.sourceforge.net/msg39091.html
-.. _deleting master on github: http://matthew-brett.github.com/pydagogue/gh_delete_master.html
+.. _deleting master on github: https://matthew-brett.github.io/pydagogue/gh_delete_master.html
 
 .. |emdash| unicode:: U+02014
diff --git a/docs/iris/src/further_topics/metadata.rst b/docs/iris/src/further_topics/metadata.rst
@@ -258,12 +258,12 @@ create a **new** instance directly from the metadata class itself,
     >>> DimCoordMetadata._make(values)
     DimCoordMetadata(standard_name=1, long_name=2, var_name=3, units=4, attributes=5, coord_system=6, climatological=7, circular=8)
 
-It is also possible to easily convert ``metadata`` to an `OrderedDict`_
+It is also possible to easily convert ``metadata`` to an `dict`_
 using the `namedtuple._asdict`_ method. This can be particularly handy when a
 standard Python built-in container is required to represent your ``metadata``,
 
     >>> metadata._asdict()
-    OrderedDict([('standard_name', 'longitude'), ('long_name', None), ('var_name', 'longitude'), ('units', Unit('degrees')), ('attributes', {'grinning face': '🙃'}), ('coord_system', GeogCS(6371229.0)), ('climatological', False), ('circular', False)])
+    {'standard_name': 'longitude', 'long_name': None, 'var_name': 'longitude', 'units': Unit('degrees'), 'attributes': {'grinning face': '🙃'}, 'coord_system': GeogCS(6371229.0), 'climatological': False, 'circular': False}
 
 Using the `namedtuple._replace`_ method allows you to create a new metadata
 class instance, but replacing specified members with **new** associated values,
@@ -943,7 +943,7 @@ such as a `dict`_,
 
     >>> mapping = latitude.metadata._asdict()
     >>> mapping
-    OrderedDict([('standard_name', 'latitude'), ('long_name', None), ('var_name', 'latitude'), ('units', Unit('degrees')), ('attributes', {}), ('coord_system', GeogCS(6371229.0)), ('climatological', False), ('circular', False)])
+    {'standard_name': 'latitude', 'long_name': None, 'var_name': 'latitude', 'units': Unit('degrees'), 'attributes': {}, 'coord_system': GeogCS(6371229.0), 'climatological': False, 'circular': False}
     >>> longitude.metadata = mapping
     >>> longitude.metadata
     DimCoordMetadata(standard_name='latitude', long_name=None, var_name='latitude', units=Unit('degrees'), attributes={}, coord_system=GeogCS(6371229.0), climatological=False, circular=False)
@@ -1000,7 +1000,6 @@ values. All other metadata members will be left unaltered.
 .. _NetCDF: https://www.unidata.ucar.edu/software/netcdf/
 .. _NetCDF CF Metadata Conventions: https://cfconventions.org/
 .. _NumPy: https://github.com/numpy/numpy
-.. _OrderedDict: https://docs.python.org/3/library/collections.html#collections.OrderedDict
 .. _Parametric Vertical Coordinate: https://cfconventions.org/Data/cf-conventions/cf-conventions-1.8/cf-conventions.html#parametric-vertical-coordinate
 .. _rich comparison: https://www.python.org/dev/peps/pep-0207/
 .. _SciTools/iris: https://github.com/SciTools/iris

diff --git a/docs/iris/src/installing.rst b/docs/iris/src/installing.rst
@@ -16,8 +16,8 @@ any WSL_ distributions.
 
 .. _WSL: https://docs.microsoft.com/en-us/windows/wsl/install-win10
 
-.. note:: Iris currently supports and is tested against **Python 3.6** and
-          **Python 3.7**.
+.. note:: Iris is currently supported and tested against Python ``3.6``,
+          ``3.7``, and ``3.8``.
 
 
 .. _installing_using_conda:

diff --git a/lib/iris/coords.py b/lib/iris/coords.py
@@ -579,7 +579,21 @@ def shape(self):
         return self._values_dm.shape
 
     def xml_element(self, doc):
-        """Return a DOM element describing this metadata."""
+        """
+        Create the :class:`xml.dom.minidom.Element` that describes this
+        :class:`_DimensionalMetadata`.
+
+        Args:
+
+        * doc:
+            The parent :class:`xml.dom.minidom.Document`.
+
+        Returns:
+            The :class:`xml.dom.minidom.Element` that will describe this
+            :class:`_DimensionalMetadata`, and the dictionary of attributes
+            that require to be added to this element.
+
+        """
         # Create the XML element as the camelCaseEquivalent of the
         # class name.
         element_name = type(self).__name__
@@ -882,6 +896,20 @@ def cube_dims(self, cube):
         return cube.cell_measure_dims(self)
 
     def xml_element(self, doc):
+        """
+        Create the :class:`xml.dom.minidom.Element` that describes this
+        :class:`CellMeasure`.
+
+        Args:
+
+        * doc:
+            The parent :class:`xml.dom.minidom.Document`.
+
+        Returns:
+            The :class:`xml.dom.minidom.Element` that describes this
+            :class:`CellMeasure`.
+
+        """
         # Create the XML element as the camelCaseEquivalent of the
         # class name
         element = super().xml_element(doc=doc)
@@ -2229,14 +2257,26 @@ def nearest_neighbour_index(self, point):
         return result_index
 
     def xml_element(self, doc):
-        """Return a DOM element describing this Coord."""
+        """
+        Create the :class:`xml.dom.minidom.Element` that describes this
+        :class:`Coord`.
+
+        Args:
+
+        * doc:
+            The parent :class:`xml.dom.minidom.Document`.
+
+        Returns:
+            The :class:`xml.dom.minidom.Element` that will describe this
+            :class:`DimCoord`, and the dictionary of attributes that require
+            to be added to this element.
+
+        """
         # Create the XML element as the camelCaseEquivalent of the
         # class name
         element = super().xml_element(doc=doc)
 
-        element.setAttribute("points", self._xml_array_repr(self.points))
-
-        # Add bounds handling
+        # Add bounds, points are handled by the parent class.
         if self.has_bounds():
             element.setAttribute("bounds", self._xml_array_repr(self.bounds))
 
@@ -2613,7 +2653,20 @@ def is_monotonic(self):
         return True
 
     def xml_element(self, doc):
-        """Return DOM element describing this :class:`iris.coords.DimCoord`."""
+        """
+        Create the :class:`xml.dom.minidom.Element` that describes this
+        :class:`DimCoord`.
+
+        Args:
+
+        * doc:
+            The parent :class:`xml.dom.minidom.Document`.
+
+        Returns:
+            The :class:`xml.dom.minidom.Element` that describes this
+            :class:`DimCoord`.
+
+        """
         element = super().xml_element(doc)
         if self.circular:
             element.setAttribute("circular", str(self.circular))
@@ -2754,7 +2807,17 @@ def __add__(self, other):
 
     def xml_element(self, doc):
         """
-        Return a dom element describing itself
+        Create the :class:`xml.dom.minidom.Element` that describes this
+        :class:`CellMethod`.
+
+        Args:
+
+        * doc:
+            The parent :class:`xml.dom.minidom.Document`.
+
+        Returns:
+            The :class:`xml.dom.minidom.Element` that describes this
+            :class:`CellMethod`.
 
         """
         cellMethod_xml_element = doc.createElement("cellMethod")

diff --git a/lib/iris/cube.py b/lib/iris/cube.py
@@ -225,6 +225,7 @@ def __getslice__(self, start, stop):
 
     def xml(self, checksum=False, order=True, byteorder=True):
         """Return a string of the XML that this list of cubes represents."""
+
         doc = Document()
         cubes_xml_element = doc.createElement("cubes")
         cubes_xml_element.setAttribute("xmlns", XML_NAMESPACE_URI)
@@ -239,6 +240,7 @@ def xml(self, checksum=False, order=True, byteorder=True):
         doc.appendChild(cubes_xml_element)
 
         # return our newly created XML string
+        doc = Cube._sort_xml_attrs(doc)
         return doc.toprettyxml(indent="  ")
 
     def extract(self, constraints):
@@ -755,6 +757,59 @@ class Cube(CFVariableMixin):
     #: is similar to Fortran or Matlab, but different than numpy.
     __orthogonal_indexing__ = True
 
+    @classmethod
+    def _sort_xml_attrs(cls, doc):
+        """
+        Takes an xml document and returns a copy with all element
+        attributes sorted in alphabetical order.
+
+        This is a private utility method required by iris to maintain
+        legacy xml behaviour beyond python 3.7.
+
+        Args:
+
+        * doc:
+            The :class:`xml.dom.minidom.Document`.
+
+        Returns:
+            The :class:`xml.dom.minidom.Document` with sorted element
+            attributes.
+
+        """
+        from xml.dom.minidom import Document
+
+        def _walk_nodes(node):
+            """Note: _walk_nodes is called recursively on child elements."""
+
+            # we don't want to copy the children here, so take a shallow copy
+            new_node = node.cloneNode(deep=False)
+
+            # Versions of python <3.8 order attributes in alphabetical order.
+            # Python >=3.8 order attributes in insert order.  For consistent behaviour
+            # across both, we'll go with alphabetical order always.
+            # Remove all the attribute nodes, then add back in alphabetical order.
+            attrs = [
+                new_node.getAttributeNode(attr_name).cloneNode(deep=True)
+                for attr_name in sorted(node.attributes.keys())
+            ]
+            for attr in attrs:
+                new_node.removeAttributeNode(attr)
+            for attr in attrs:
+                new_node.setAttributeNode(attr)
+
+            if node.childNodes:
+                children = [_walk_nodes(x) for x in node.childNodes]
+                for c in children:
+                    new_node.appendChild(c)
+
+            return new_node
+
+        nodes = _walk_nodes(doc.documentElement)
+        new_doc = Document()
+        new_doc.appendChild(nodes)
+
+        return new_doc
+
     def __init__(
         self,
         data,
@@ -3399,6 +3454,7 @@ def xml(self, checksum=False, order=True, byteorder=True):
         doc.appendChild(cube_xml_element)
 
         # Print our newly created XML
+        doc = self._sort_xml_attrs(doc)
         return doc.toprettyxml(indent="  ")
 
     def _xml_element(self, doc, checksum=False, order=True, byteorder=True):

diff --git a/lib/iris/plot.py b/lib/iris/plot.py
@@ -1073,6 +1073,18 @@ def contourf(cube, *args, **kwargs):
             # any boundary shift.
             zorder = result.collections[0].zorder - 0.1
             axes = kwargs.get("axes", None)
+
+            # Workaround for cartopy#1780.  We do not want contour to shrink
+            # extent.
+            if axes is None:
+                _axes = plt.gca()
+            else:
+                _axes = axes
+
+            # Subsequent calls to dataLim.update_from_data_xy should not ignore
+            # current extent.
+            _axes.dataLim.ignore(False)
+
             contour(
                 cube,
                 levels=levels,

diff --git a/lib/iris/tests/__init__.py b/lib/iris/tests/__init__.py
@@ -573,6 +573,10 @@ def assertXMLElement(self, obj, reference_filename):
         """
         doc = xml.dom.minidom.Document()
         doc.appendChild(obj.xml_element(doc))
+        # sort the attributes on xml elements before testing against known good state.
+        # this is to be compatible with stored test output where xml attrs are stored in alphabetical order,
+        # (which was default behaviour in python <3.8, but changed to insert order in >3.8)
+        doc = iris.cube.Cube._sort_xml_attrs(doc)
         pretty_xml = doc.toprettyxml(indent="  ")
         reference_path = self.get_result_path(reference_filename)
         self._check_same(

diff --git a/lib/iris/tests/results/analysis/sqrt.cml b/lib/iris/tests/results/analysis/sqrt.cml
@@ -39,6 +39,6 @@
       </coord>
     </coords>
     <cellMethods/>
-    <data checksum="0x09ef96ca" dtype="float64" shape="(73, 96)"/>
+    <data dtype="float64" shape="(73, 96)" state="loaded"/>
   </cube>
 </cubes>